Contents

 
• List of Figures
• List of Tables
• 1 Introduction
  • 1.1 For more information on VMD and MDScope
  • 1.2 Contacting the authors
  • 1.3 Credits and program reference
  • 1.4 Registering VMD
  • 1.5 Acknowledgments
  • 1.6 Disclaimer
• 2 Tutorials
  • 2.1 Rapid Introduction to VMD
  • 2.2 Viewing a molecule: Myoglobin
  • 2.3 Rendering an Image
  • 2.4 A Quick Animation
  • 2.5 An Introduction to Atom Selection
  • 2.6 Comparing Two Structures
• 3 User Interface Components
  • 3.1 Using the Mouse in the Graphics Window
    • 3.1.1 The Popup Menu
      • Mouse Mode Submenu
      • Pick Item Mode Submenu
      • Display Modes Submenu
      • Fit Submenu
      • Labels Submenu
      • Animate Scene Submenu
      • Spin/Rock Scene Submenu
      • Stop Rotation
      • Reset View
      • Show Form Submenu
      • Hide Form Submenu
      • Help
      • Quit Submenu
      • Play File
      • Save Config
    • 3.1.2 Atom/Molecule Specific Popup Menu
      • Center
      • Pick
      • Info
    • 3.1.3 Mol Status
    • 3.1.4 Atom Selection
    • 3.1.5 Rendering Method
    • 3.1.6 Coloring Method
    • 3.1.7 Delete Rep.
    • 3.1.8 Hot Keys
  • 3.2 Using the Forms library
    • 3.2.1 Buttons
    • 3.2.2 Sliders
    • 3.2.3 Choosers
    • 3.2.4 Text Entry Areas
    • 3.2.5 Browsers
    • 3.2.6 File Browser
  • 3.3 Description of each VMD form
    • 3.3.1 Main Form
    • 3.3.2 Molecules (Mol) Form
      • Loading a New Molecule
      • The Molecule List browser
      • Changing the Molecule's Status
      • Deleting a Molecule
    • 3.3.3 Files Form
    • 3.3.4 Graphics Form
      • Image Controls
      • Atom Name Lists
      • Changing Views
    • 3.3.5 Animate Form
      • Animation Speed
      • Jumping to Specific Frames
      • Looping Styles
    • 3.3.6 Edit Animation Form
      • Reading Frames
      • Writing Frames
      • Deleting Frames
      • Amount Chooser
    • 3.3.7 Labels Form
      • Label categories
      • Modifying or deleting a label
      • Plotting a label's value
    • 3.3.8 Display Form
    • 3.3.9 Color Form
      • Changing the RGB Value of a Color
      • Color Scale
    • 3.3.10 Render Form
      • Rendering
      • Caution
    • 3.3.11 Tracker Form
      • Trackers
      • Tools
    • 3.3.12 Remote Form
      • Establishing a Connection
      • Starting a New Simulation
      • Once a Connection is Made
    • 3.3.13 Sim Form
      • Modifiable Parameters
  • 3.4 Other User Interfaces
    • 3.4.1 3D
    • 3.4.2 External Interfaces
    • 3.4.3 Using the remote commands
    • 3.4.4 Speech
    • 3.4.5 Gesture
    • 3.4.6 Other Uses
• 4 Loading A Molecule
  • 4.1 Babel interface
  • 4.2 What happens when a file is loaded?
  • 4.3 Raster3D file format
  • 4.4 Raster3D Caveats
• 5 Molecular Drawing Methods
  • 5.1 Lines
  • 5.2 Bonds
  • 5.3 CPK
  • 5.4 Points
  • 5.5 VDW
  • 5.6 Dotted
  • 5.7 Solvent
  • 5.8 Tube
  • 5.9 Trace
  • 5.10 Licorice
  • 5.11 Ribbon
  • 5.12 Surf
  • 5.13 Cartoon
  • 5.14 MSMS
  • 5.15 HBonds
  • 5.16 Off
• 6 Coloring Molecules and Objects
  • 6.1 Color categories
  • 6.2 Coloring Methods
    • 6.2.1 Coloring by color categories
    • 6.2.2 Color scale
  • 6.3 Transparency
  • 6.4 VMD Script Commands for Colors
    • 6.4.1 Adjusting the degree of transparency
    • 6.4.2 Changing the color scale definitions
    • 6.4.3 Creating a set of black-and-white color definitions
    • 6.4.4 Revert all RGB values to defaults
    • 6.4.5 Setting the transparent colors according to solid
    • 6.4.6 Making the molecule to show up slowly
    • 6.4.7 Querying VMD for Color Information
• 7 VMD Atom Selection Language
  • 7.1 Definition of Keywords and Functions
  • 7.2 Boolean Keywords
  • 7.3 Short Circuiting
  • 7.4 Quoting with Single Quotes
  • 7.5 Double Quotes and Regular Expressions
  • 7.6 Comparison selections
  • 7.7 Comparison Operators
  • 7.8 Other selections
    • 7.8.1 sequence
    • 7.8.2 within and same
    • 7.8.3 annmm
  • 7.9 Referencing Tcl data
    • 7.9.1 $references
    • 7.9.2 @references
    • 7.9.3 The differences
• 8 Creating Output Raster Images
  • 8.1 Creating an Output Image File
  • 8.2 Known Problems
  • 8.3 One Step Printing
• 9 Viewing Modes
  • 9.1 Perspective/Orthographic views
  • 9.2 Monoscopic Modes
  • 9.3 Stereoscopic Modes
    • 9.3.1 Side-By-Side and Cross-Eyed Stereo
    • 9.3.2 Crystal Eyes Stereo
      • Stereo in a window (aka new-style stereo):
      • Regular stereo mode:
    • 9.3.3 Problems with stereo on Indigo2 machines
    • 9.3.4 Stereo Parameters
  • 9.4 Making Stereo Raster Images
• 10 Interactive Molecular Dynamics Display Using MDComm
  • 10.1 How the Connection Works
  • 10.2 Installing VMD Remote Connection Components
  • 10.3 Installing NAMD Remote Connection Components
  • 10.4 When Problems Occur
• 11 Text User Interface
  • 11.1 Using text commands
  • 11.2 Tcl/Tk
  • 11.3 Core Text Commands
    • 11.3.1 animate
    • 11.3.2 axes
    • 11.3.3 color
    • 11.3.4 colorinfo
    • 11.3.5 debug
    • 11.3.6 display
    • 11.3.7 echo
    • 11.3.8 exit
    • 11.3.9 external
    • 11.3.10 help
    • 11.3.11 label
    • 11.3.12 light
    • 11.3.13 logfile
    • 11.3.14 menu
    • 11.3.15 mol
    • 11.3.16 molecule
    • 11.3.17 mouse
    • 11.3.18 play
    • 11.3.19 quit
    • 11.3.20 remote
    • 11.3.21 render
    • 11.3.22 rock
    • 11.3.23 rotate
    • 11.3.24 scale
    • 11.3.25 sim
    • 11.3.26 simulation
    • 11.3.27 stage
    • 11.3.28 tracker
    • 11.3.29 translate
    • 11.3.30 user
    • 11.3.31 vmdlog
    • 11.3.32 vmdinfo
    • 11.3.33 wait
• 12 Vectors and Matrices
  • 12.1 Vectors
  • 12.2 Matrix routines
  • 12.3 Multiplying vectors and matrices
  • 12.4 Misc. functions and values
    • What's missing
• 13 User-Defined Graphics
  • 13.1 Introduction
  • 13.2 Tutorials and Examples
    • 13.2.1 Drawing a graph
    • 13.2.2 Triangles
    • 13.2.3 Draw a surface plot
    • 13.2.4 Drawing a box around a molecule
    • 13.2.5 Adding a label
    • 13.2.6 Interface to picking
    • 13.2.7 Animation
  • 13.3 Graphics
  • 13.4 Draw and Drawing Extensions
• 14 Molecular information: molinfo and atomselect
  • 14.1 molinfo
    • 14.1.1 Using molinfo to access the molecule list
    • 14.1.2 Using molinfo to access information about a molecule
  • 14.2 Atom information
  • 14.3 Analysis scripts
• 15 Tips and Tricks
  • 15.1 Customizing the Popup Menu and the Hot Keys
    • 15.1.1 Customizing the popup menu
    • 15.1.2 Customizing the Hot Keys
    • 15.1.3 Automatically loading customization commands
  • 15.2 Using VMD as a WWW Client (for chemical/* documents)
    • 15.2.1 MIME types
      • Helper Applications
    • 15.2.2 Setting up your .mailcap
    • 15.2.3 Example sites
  • 15.3 Making a Movie
  • 15.4 Coloring Trick - Override a Coloring Category
  • 15.5 Some Nice Represenations
  • 15.6 Finding Contact Residues
  • 15.7 Tcl Logging
  • 15.8 Remote Control of VMD
  • 15.9 Controlling One VMD With Another
• 16 Advanced Script Writing
  • 16.1 Drawing a distance matrix
  • 16.2 Analysis of PDB files
  • 16.3 save/load VMD state information
  • 16.4 Currently picked molecule/atom
  • 16.5 Trace on the pick variables
    • 16.5.1 Information about the picked atom
    • 16.5.2 Making a sphere appear when an atom is picked
    • 16.5.3 Drawing a line from the eye to the picked atom
  • 16.6 Trajectory frames
    • 16.6.1 Animating the secondary structure
    • 16.6.2 Viewing selections which change during an animation
    • 16.6.3 Simulation frames
  • 16.7 RMSD and best-fit alignments
    • 16.7.1 RMSD Computation
    • 16.7.2 Computing the Alignment
    • 16.7.3 A simulation example script
• 17 Customizing VMD Sessions
  • 17.1 Command-Line Options
  • 17.2 Environment Variables
  • 17.3 Startup Files
    • 17.3.1 Core Script Files
    • 17.3.2 User Script Files
    • 17.3.3 .vmd_init File
    • 17.3.4 .vmdrc File
• 18 Future Plans
• Index
• About this document ...